16-56610738-C-A

Variant names:

• chr16-56610738-C-A
• rs1580833
• ENST00000569778.1:n.60+578G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000569778.1(ENSG00000260823):​n.60+578G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 152,030 control chromosomes in the GnomAD database, including 8,558 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.32 (8558 hom., cov: 32)
• Consequence: ENSG00000260823 ENST00000569778.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563

Genes affected

ENSG00000260823 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260823	ENST00000569778.1	n.60+578G>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49165 AN: 151912 Hom.: 8542 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.333

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.324 AC: 49212 AN: 152030 Hom.: 8558 Cov.: 32 AF XY: 0.328 AC XY: 24396 AN XY: 74314

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.336

Alfa AF: 0.312 Hom.: 1049

Bravo AF: 0.335

Asia WGS AF: 0.520 AC: 1807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1580833; hg19: chr16-56644650;